Illuminating the role of whole genome sequencing in produce safety

Whole genome sequencing (WGS) is rapidly becoming the gold standard for foodborne outbreak investigations by public health agencies around the world. However, as WGS continues to be developed as a tool it needs to be refined to maximize its potential, and thus reach the ultimate goal of speeding up investigations. Therefore, the goal of this project is to provide data to public health agencies like the FDA to improve the use of WGS as an outbreak investigation tool. Overall, this project will help to refine WGS as a tool for outbreak investigations for public health agencies to use during outbreaks. Furthermore, this project can be use by the produce industry to implement WGS for internal source tracking to identify “resident” versus “transient” pathogens, sources of contamination for either, and a better understanding of the breakdowns or gaps in prevention, thus improving produce safety by closing these gaps.

Technical Abstract

Due to its higher resolution, whole genome sequencing (WGS) is rapidly becoming the new gold standard for foodborne outbreak investigations. But, there is still a continued effort to refine the implementation of WGS thus improving accuracy while reducing investigation time. Foodborne pathogens often cycle around defined regions, which was a major factor behind the creation of the FDA’s GenomeTrakr network, because if you can match clinical cases to a defined region then the investigation can quickly narrow the search to that region. GenomeTrakr involves state, federal, commercial and international laboratories genome sequencing regional foodborne pathogens to create a public database of regional genomic pathogen profiles for investigations. However, as the pathogens continue to cycle through the environment in those regions the genomes may accrue mutations that could alter the regional genomic pathogen profile, which could limit the positive impact of GenomeTrakr on investigations. The goal of this project is to determine the mutation rates of Salmonella, Listeria, and Escherichia coli O157:H7 during long-term persistence in agricultural soil and irrigation water maintained under different geographical conditions. Understanding these mutational rates will help improve the development of GenomeTrakr for regional identification during an outbreak investigation. Furthermore, data from this project will assist the produce industry in developing WGS for internal source tracking to identify “resident” versus “transient” pathogens, sources of contamination for either, and better understand the breakdowns or gaps in prevention methods, thus improving produce safety by closing these gaps.